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Sample GSM27387 Query DataSets for GSM27387
Status Public on Oct 24, 2004
Title Cotyledon dark, n3
Sample type RNA
 
Channel 1
Source name cultured cell
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name Cotyledon dark
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Cotyledon dark vs cultured cell
 
Submission date Jul 26, 2004
Last update date May 27, 2005
Contact name Ligeng Ma
E-mail(s) ligeng.ma@yale.edu
Phone 203-432-8909
Organization name Yale University
Department Molecular, Cellular & Developmental Biology
Lab Deng Lab
Street address 165 Prospect
City NEW HAVEN
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL988
Series (1)
GSE1599 Arabidopsis Transcriptome

Data table header descriptions
ID_REF
CH1_median Channel 1 (635 nm, Cy5, Reference) median pixel intensity
CH2_median Channel 2 (532 nm, Cy3, Experiment) median pixel intensity
CH1_back Channel 1 Background
CH2_back Channel 2 Background
CH1_MEAN Channel 1 Mean
CH2_MEAN
CH1_SD Channel 1 Standard Deviation
CH2_SD Channel 2 Standard Deviation
pixels Number of pixels used to determine signal.
bpixels Number of pixels used to determine background.
x X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
diameter diameter in īm of the feature-indicator
%>CH1_back+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 1
%>CH1_back+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 1
%>CH2_back+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 2
%>CH2_back+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 2
CH1_%Sat percentage of pixel saturation within feature for Channel 1
CH2_%Sat percentage of pixel saturation within feature for Channel 2
QUALITY
flag An extension of GenePix 3.0 flags described at http://twiki.med.yale.edu/twiki/bin/view/YMD/YMDFlagFields
ratio_calc (CH1_median-CH1_back)/(CH2_median-CH2_back)
VALUE log ratio (log2 of PRE_VALUE)
norm_factor Normalization factor calculated as described at http://twiki.med.yale.edu/twiki/bin/view/YMD/NormalizationAndFilterMethods
PRE_VALUE [(Experiment channel median intensity - background)/(Reference channel median intensity - background)]*(norm_factor)

Data table
ID_REF CH1_median CH2_median CH1_back CH2_back CH1_MEAN CH2_MEAN CH1_SD CH2_SD pixels bpixels x y diameter %>CH1_back+1SD %>CH1_back+2SD %>CH2_back+1SD %>CH2_back+2SD CH1_%Sat CH2_%Sat QUALITY flag ratio_calc VALUE norm_factor PRE_VALUE
3203713 3672 1364 124 177 4071 1373 1290 349 80 433 4590 10360 110 100 100 100 100 0 0 1 0 .335 -1.5777673 1.000 .335
3203745 4270 637 125 189 4304 639 887 122 80 466 3190 10530 110 100 100 100 100 0 0 1 0 .108 -3.2108973 1.000 .108
3204483 143 217 128 173 141 218 55 43 80 395 9280 8970 100 25 8 56 23 0 0 1 -50 2.933 1.5523773 1.000 2.933
3204499 229 272 125 180 229 278 65 49 52 291 10680 8970 80 75 32 90 61 0 0 1 0 .885 -0.1762513 1.000 .885
3204567 144 198 123 165 151 201 56 47 80 418 8230 9310 100 33 10 41 15 0 0 1 -50 1.571 0.6516833 1.000 1.571
3205269 229 244 129 198 247 248 100 53 52 322 10840 11780 80 69 50 57 26 0 0 1 0 .460 -1.1202943 1.000 .460
3205335 644 357 131 192 668 362 216 81 80 467 8210 12120 110 100 100 95 85 0 0 1 0 .322 -1.6348673 1.000 .322
3205367 140 229 125 191 141 235 48 49 80 473 6820 12290 100 21 3 41 16 0 0 1 -50 2.533 1.3408473 1.000 2.533
3206081 286 292 136 162 300 298 110 71 120 446 14950 10600 120 82 64 92 85 0 0 1 0 .867 -0.2058963 1.000 .867
3206919 149 240 129 179 148 241 54 44 80 416 17250 9530 100 21 6 68 35 0 0 1 -50 3.050 1.6088093 1.000 3.050
3206927 986 339 140 203 1008 344 348 80 120 542 17960 9540 120 100 100 87 57 0 0 1 0 .161 -2.6348673 1.000 .161
3206963 289 288 133 186 293 286 88 60 80 494 16910 9710 110 88 72 86 55 0 0 1 0 .654 -0.6126373 1.000 .654
3206989 328 557 137 205 327 538 96 125 80 440 19190 9710 110 92 75 100 100 0 0 1 0 1.843 0.8820563 1.000 1.843
3207691 238 408 134 191 246 405 72 98 80 396 17600 12330 100 78 43 95 92 0 0 1 0 2.087 1.0614313 1.000 2.087
3203717 543 232 119 165 541 235 142 50 80 427 4940 10370 100 100 100 70 37 0 0 1 0 .158 -2.6620043 1.000 .158
3203769 258 1055 125 166 273 1067 78 199 80 452 5290 10540 110 92 76 100 100 0 0 1 0 6.684 2.7407123 1.000 6.684
3205265 175 201 126 168 185 205 67 38 80 420 10490 11790 100 47 22 41 8 0 0 1 -50 .673 -0.5713223 1.000 .673
3205347 152 229 124 178 161 224 57 43 80 438 9260 12130 100 38 17 65 28 0 0 1 -50 1.821 0.8647313 1.000 1.821
3206101 186 4497 124 184 187 4430 74 1814 120 397 12520 10760 120 50 22 94 92 0 0 1 0 69.565 6.1202903 1.000 69.565
3206121 161 310 129 174 188 320 150 64 80 399 14250 10770 110 40 15 97 87 0 0 1 0 4.250 2.0874633 1.000 4.250

Total number of rows: 27648

Table truncated, full table size 2973 Kbytes.




Supplementary data files not provided
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